GeneSet Analysis

As KIRC and KIRP were analyzed under Kidney-RCC in Kahraman study, we have merged those two cancer types in Vitting and Climente-Gonzales studies in our analysis to detect the overlaps.
## Loading required package: dplyr
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Loading required package: grid
## Loading required package: ggplot2

##        V1
## 1     TNC
## 2   ATXN3
## 3  FAM76B
## 4    CAP2
## 5  PNPLA7
## 6    PPAN
## 7   DACH1
## 8   CPLX1
## 9    SKA2
## 10  BICD2
## 11  HOXC6

##            V1
## 1    C19orf60
## 2      OSBPL5
## 3        CD44
## 4     ZFYVE16
## 5        TLE2
## 6  ST6GALNAC1
## 7       LIMS2
## 8       CALD1
## 9        PNKD
## 10       SHC2
## 11       RIN2
## 12      MYO10
## 13    C7orf50
## 14        AK3
## 15    RABGEF1
## 16     TSPAN7
## 17      FMNL3
## 18       ING2
## 19       PCCA
## 20     SH3BGR
## 21     BTN3A2

##         V1
## 1     CD44
## 2    RC3H2
## 3  CEACAM1
## 4    NRCAM
## 5   CDADC1
## 6    GSPT1
## 7     CAV1
## 8    DNMBP
## 9     LIPA
## 10   NCOA7
## 11    KTN1
## 12  PDGFRA
## 13   BCAR3
## 14    RGS3
## 15   TARS2
## 16 ZNF385B
## 17   OBSCN
## 18    NAGS
## 19   BSCL2
## 20  PCMTD1
## 21   AP1S2
## 22    EXD3
## 23   ZNF44
## 24    WWP2
## 25  CTNND1
## 26  SCAMP5

##       V1
## 1  KIF22
## 2   NXT2
## 3   NT5E
## 4   GBAS
## 5  PANK1
## 6  CXADR
## 7  MFAP4
## 8  NUDT6
## 9   FGGY
## 10  AQP1

##          V1
## 1     SPAG9
## 2       LSR
## 3     ITM2C
## 4     CXADR
## 5     CPLX1
## 6 TNFRSF10C

##         V1
## 1   CASP10
## 2  SDCCAG8
## 3    ATXN3
## 4    CECR1
## 5   DYRK1B
## 6      LSR
## 7     MEST
## 8     GAB1
## 9    CNOT2
## 10   MKLN1
## 11 SHROOM2
## 12   NTRK2
## 13     DST
## 14  IL17RE
## 15 PPFIBP2
## 16    WWOX
## 17  CTNND1

##      V1
## 1 VAMP1

##         V1
## 1      CFH
## 2 C1orf198
## 3  FAM174B

##          V1
## 1  C19orf60
## 2    MLXIPL
## 3   PLEKHH1
## 4    ATP2B4
## 5  SLC9A3R2
## 6     FGFR2
## 7    RASSF1
## 8    ATP2B1
## 9     BAZ2A
## 10  SMARCA2
## 11    EPS15
## 12    IPO11
## 13     MMP2
## 14    CECR1
## 15     MFNG
## 16    PATZ1
## 17     ASB9
## 18     FLT1
## 19    TAF1C
## 20    ILVBL
## 21   TIMM50
## 22    ADAP1
## 23     CAV1
## 24    DOCK8
## 25    DNMBP
## 26     LIPA
## 27    SHOC2
## 28    KLHL2
## 29  ST3GAL4
## 30      MVK
## 31   SCNN1A
## 32   BTN3A3
## 33    DOCK7
## 34     MXI1
## 35    ARAP3
## 36    ACOT9
## 37   IQSEC2
## 38     PSD4
## 39     EML2
## 40    TRPM4
## 41   EPS8L1
## 42   DIAPH1
## 43    DMGDH
## 44   PDGFRA
## 45     BIVM
## 46    ITM2C
## 47     CIB2
## 48     BIN1
## 49     FPGS
## 50    BCAR3
## 51    NCOA4
## 52   RNF185
## 53    SSBP2
## 54    DCDC2
## 55   ZNF185
## 56   TM7SF2
## 57     SCOC
## 58   ABI3BP
## 59    CXADR
## 60  RABGEF1
## 61    RMND1
## 62    AIFM1
## 63  SLC35B2
## 64    KALRN
## 65     MUM1
## 66  TBC1D24
## 67    STK36
## 68   HDAC11
## 69    MYO5B
## 70    TMCC1
## 71  GOLGA8A
## 72  EFCAB4A
## 73  GRAMD1C
## 74    LIMK2
## 75    SPNS3
## 76    AFMID
## 77    RBM33
## 78  FAM174B
## 79     MITF
## 80   ZNF559
## 81  TMEM201
## 82    ZNF44
## 83     WWP2
## 84   SCAMP5
## 85    PPME1
## 86     CUX1

Isoform Switch Analysis

##   Normal_Isoform_Cancer_Isoform
## 1             uc003gbj_uc003gbi
## 2             uc004aso_uc004asp
## 3             uc003ncb_uc011djb

##   Normal_Isoform_Cancer_Isoform
## 1             uc002vhm_uc002vhq

##   Normal_Isoform_Cancer_Isoform
## 1             uc002otv_uc002otw
## 2             uc001mvx_uc001mvw
## 3             uc002unj_uc002unn

##   Normal_Isoform_Cancer_Isoform
## 1             uc003iew_uc003iex
## 2             uc003tbv_uc010kwf
## 3             uc003pko_uc010kbr
## 4             uc003tre_uc003trf
## 5             uc002yki_uc002ykj
## 6             uc001kgn_uc001kgo
## 7             uc001qyu_uc001qyt

##   Normal_Isoform_Cancer_Isoform
## 1             uc003gbj_uc003gbi
## 2             uc002yki_uc002ykj

##   Normal_Isoform_Cancer_Isoform
## 1             uc002uxj_uc010ftb
## 2             uc002nym_uc002nyn
## 3             uc003vqg_uc003vqc

## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)

## [1] Normal_Isoform_Cancer_Isoform
## <0 rows> (or 0-length row.names)

##    Normal_Isoform_Cancer_Isoform
## 1              uc001kza_uc001kyy
## 2              uc003akb_uc003ake
## 3              uc004evg_uc004evi
## 4              uc002bdb_uc002bdc
## 5              uc002cok_uc002coi
## 6              uc001dpx_uc001dpy
## 7              uc002yki_uc002ykj
## 8              uc004bsg_uc004bsi
## 9              uc003aks_uc003akr
## 10             uc003eas_uc003eaq

Normal Isoform Analysis

## [1] "uc003gbj" "uc004aso" "uc003ncb" "uc001sev"

##  [1] "uc002tpa" "uc001voo" "uc001lxk" "uc002njv" "uc002vhm" "uc002jsh"
##  [7] "uc003kgq" "uc002loq" "uc003jft" "uc003ziq" "uc004deg" "uc002yya"

##  [1] "uc002otv" "uc001qba" "uc004cxi" "uc004cmp" "uc001mvx" "uc001nup"
##  [7] "uc003vfc" "uc003han" "uc002unj" "uc002ies"

##  [1] "uc003iew" "uc003tbv" "uc002gvt" "uc003pko" "uc003tre" "uc002yki"
##  [7] "uc001kgn" "uc003hzc" "uc001qyu" "uc004eof"

## [1] "uc002vqz" "uc003gbj" "uc003xcy" "uc002yki"

## [1] "uc002uxj" "uc002nym" "uc002ffk" "uc004csu" "uc011chq" "uc009zro" "uc003vqg"
## [8] "uc003btw"

## character(0)
## [1] "uc001hub" "uc010boe"
## Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [4455].
## Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [587].

##  [1] "uc001csq" "uc001kzl" "uc003irb" "uc009zvk" "uc001kza" "uc002pcn"
##  [7] "uc001vps" "uc002vqz" "uc002tob" "uc003akb" "uc001oct" "uc004evg"
## [13] "uc003oxd" "uc002cqk" "uc010boe" "uc003vcm" "uc003sjo" "uc001lrv"
## [19] "uc002njv" "uc003dab" "uc002zmj" "uc002pmw" "uc003ass" "uc003llm"
## [25] "uc002bdb" "uc003tyn" "uc002cok" "uc002nam" "uc001dpx" "uc002yki"
## [31] "uc001xjl" "uc003han" "uc004bsg" "uc011che" "uc002jva" "uc003aks"
## [37] "uc004cwk" "uc004dap" "uc002tjc" "uc002qis" "uc003kfs" "uc003ndx"
## [43] "uc003eas" "uc001apy"

Cancer Isoform Analysis

## [1] "uc003gbi" "uc004asp" "uc002uhz" "uc011djb"

## [1] "uc003sju" "uc003tvh" "uc002uhz" "uc002vhq" "uc009xkg"

## [1] "uc002otw" "uc003qai" "uc001mvw" "uc001dpy" "uc002unn"

## [1] "uc003iex" "uc010kwf" "uc010kbr" "uc003trf" "uc002ykj" "uc001kgo" "uc001qyt"
## [8] "uc002dts"

## [1] "uc003gbi" "uc002ykj"

## [1] "uc010ftb" "uc002nyn" "uc003pdc" "uc003vqc"

## character(0)

## [1] "uc009xkg"

## [1] "uc001kyy" "uc003ake" "uc003tvh" "uc003ehk" "uc002bdc" "uc001dpy" "uc002ykj"
## [8] "uc003akr" "uc003eaq"